A headset that is 1mm thicker on the bottom cup than the builder designed the frame for could cause this even. And since you have a replacement fork I would say that that is likely responsible. The height on the fork is likely different by a mm or two. Different fork crowns are different thicknesses, which means different height forks and the frame was built according to that particular fork... So I am not surprised. You should be pleased that the difference is so minuscule and you have such a closely matching fork.